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The tricky part is that if you look at the first line in the file
hbm.xpm you are looking at the bottom row of the matrix when
displayed with gimp or after converting to xpm2ps. The same line
corresponds to the first hbond in hbn.ndx. That sentence in the
manual is therefore a bit ambiguous.<br>
<br>
Erik<br>
<br>
Carla Jamous skrev 2010-10-15 13.29:
<blockquote
cite="mid:AANLkTi=rHWw26qFy6otZ5qQPwJOYTdBVnrEZx+TzH5mq@mail.gmail.com"
type="cite">I'm sorry I don't understand, because your last answer
doesn't correspond to what's written in the manual. I'm using
gromacs 4.0.3 and the manual says:<br>
<br>
-hbm: existence matrix. Ordering is identical to that in -hbn
index file.<br>
<br>
And yes, my trajectory is concatenated the way I intended to, but
I will check anyway.<br>
<br>
Carla<br>
<br>
<div class="gmail_quote">On Fri, Oct 15, 2010 at 1:23 PM, Erik
Marklund <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<div class="im"> Carla Jamous skrev 2010-10-15 12.05:<br>
</div>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
Hi everyone,
<div>
<div class="h5"><br>
<br>
please I need some help on g_hbond.<br>
<br>
I concatenated 3 trajectories. I ran g_hbond on the
concatenated trajectory. I got the result of h_bonds.<br>
Then I wanted to run g_hbond on each of my 3
trajectories. Here, I get a different result, it means:
if I take the first 10ps of my concatenated trajectory
and I run g_hbond on these 10ps. I get some H-bonds eg.
Gly(N)...H(gly)...O<br>
but this same
H-bond doesn't appear in the first 10ps of my
concatenated trajectory's HBmap.<br>
<br>
Please does anyone have an idea where I might have done
a mistake?<br>
<br>
Thank you,<br>
Carla<br>
<br>
</div>
</div>
</blockquote>
Have you confirmed that the concaternation was done the way
you intended?
<div>
<div class="h5"><br>
<br>
-- <br>
-----------------------------------------------<br>
Erik Marklund, PhD student<br>
Dept. of Cell and Molecular Biology, Uppsala University.<br>
Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>
phone: +46 18 471 4537 fax: +46 18 511 755<br>
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</blockquote>
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<br>
</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
<a class="moz-txt-link-abbreviated" href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a> <a class="moz-txt-link-freetext" href="http://folding.bmc.uu.se/">http://folding.bmc.uu.se/</a>
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